Is it a prime time for germline genetic testing for HCC?
Authors: Takahiro Kodama, Tetsuo Takehara
Journal: Hepatology (2023)

International collaborative projects on cancer genome sequencing, such as The Cancer Genome Atlas (TCGA) and the International Cancer Genome Consortium (ICGC), have profiled cancer genomic abnormalities in more than 10,000 patients, almost completing the catalog of somatic mutations in cancer genes. Currently, cancer genome profiling via next-generation sequencing is used in routine clinical practice and helps to guide personalized cancer therapy.1 For HCC, while somatic mutations in the TERT promoter, TP53, and CTNNB1 were most frequent and recognized as core cancer drivers, infrequent mutations were also observed in hundreds of genes.2 Unfortunately, no targeted treatment exists for most of these mutated genes; thus, HCC pharmacotherapy is generally aimed at targeting angiogenesis and immune checkpoints. Together with the reduced accessibility to tumor tissue from advanced HCC patients, cancer genome profiling is not widely performed in the HCC field. Germline genetic testing has been historically performed to identify cancer predisposition syndromes, leading to a prediction of hereditary cancer risk and/or prevention by risk-reducing surgery. However, the importance of identifying germline mutations in a variety of cancer patients has been increasingly recognized, as several drugs have been recently approved, including poly(ADP-ribose) polymerase inhibitors (PARPis), for advanced ovarian cancer patients with germline BRCA1/2 alterations.3 Indeed, large-scale pan-cancer analysis of adult cancers showed that ~8% of patients had pathogenic germline variants (PGVs) in cancer susceptibility genes.4 Collectively, the National Comprehensive Cancer Network endorsed universal germline analysis of all patients with metastatic breast cancer, ovarian cancer, pancreatic cancer, and advanced prostate cancer.3,5 However, the characteristics and clinical significance of PGVs in HCC have not been fully clarified. In this issue of HEPATOLOGY, An et al.6 aimed to clarify the frequency and clinical significance of germline mutations in the DNA damage repair (DDR) pathway in HCC. To avoid bias caused by ancestry-associated differences,7 they studied a total of 592 HCC patients in their Korean and TCGA cohorts with ethnic diversity. They found that 16.2% of HCC patients held PGVs in DDR genes, while 8.8% of HCC patients held pathogenic somatic variants (PSVs) in these genes. These frequencies were also confirmed in the ICGC cohort (16.5% of 285 cases for PGVs and 12% of 1306 cases for PSVs). Patients with PGVs or PSVs in the DDR pathway had higher fractions of somatic copy number alterations and degrees of ploidy than those without, suggesting that these variants may contribute to the increase in genomic instability. Among 110 PGVs in the DDR pathway, POLQ was identified as the most frequently mutated gene and detected in 10 cases. Subsequently, they showed that patients with PGVs in DDR genes had significantly poorer disease-free survival (DFS) after hepatectomy than those without. Next, they focused on the homologous recombination (HR) pathway and evaluated the molecular and clinical characteristics of HCC with PGVs in the HR pathway. Transcriptomics-based analysis showed that tumors with PGV in the HR pathway have some molecular features, such as more proliferative and higher replication stress, than those without PGV, while they were not classified into any known molecular subclass. Interestingly, a family history of HCC was the only significant clinical variable related to the presence of PGVs in the HR pathway. It is well known that a family history of HCC is a significant risk factor for HCC development in patients with chronic liver disease,8 but its molecular mechanisms are not well understood. The above findings suggested that germline variances in the HR pathway may at least partly explain such hereditary cancer risk. An and colleagues also found that 1-quarter of PGVs in DDR genes were loss of heterozygosity, and patients with both PGVs and loss of heterozygosity in HR genes showed the worst DFS. Finally, they attempted to identify the therapeutic implications of PGVs in the HR pathway. An in silico approach using the OncoKB database suggested that PARPi may be beneficial to HCC patients with PGVs in the HR pathway, including BRCA1, BRCA2, BRIP1, BARD1, PALB2, RAD51B, and RAD54L. Indeed, they demonstrated the high sensitivity of human HCC cell lines with either mutation or RNAi-based silencing of BRCA2 to PARPi in vitro. Such high sensitivity was associated with strong DNA damage, aberrant mitotic progression, apoptosis, and impaired RAD51-mediated DNA repair, suggesting the well-known synthetic lethality caused by DDR dysfunction in PARPi-treated HR-deficient tumors. Interestingly, although patients with PGV in POLQ, the other member of the HR pathway, were not denoted as potential responders to PARPi by OncoKB, human HCC cell lines with either mutation or RNAi-based silencing of POLQ also showed great sensitivity to PARPi, suggesting that PARPi may be broadly applicable to HCC patients with PGVs in the HR pathway, which account for ~7.4% (44 of 592 HCC patients) among this study cohort. This is the first report to demonstrate a large-scale in-depth analysis of PGVs in the DDR pathway in HCC and their clinical significance. This study provides us with 2 clinically important findings. First, the frequency of PGVs in the DDR pathway is not rare, and patients with a familial history of HCC may have a high risk of harboring PGVs in the HR pathway. Considering the poor DFS of patients with PGVs in the HR genes, the detection of PGVs by genetic testing may guide better HCC surveillance for these patients. Second, HCC patients with PGVs in the HR pathway, especially the BRCA2 and POLQ genes, may be susceptible to PARPi. Considering that several PARPis are FDA-approved and available for daily practice, the detection of PGVs in the HR pathway may provide a new potent therapeutic option. Taken together, these findings may facilitate cancer genome profiling for HCC patients. The limitation of this study includes the difficulty of accurate clinical interpretation of germline variants. In this study, 1429 germline variants were excluded due to uncertain significance, which may overlook the currently unrecognized pathogenic variants. In contrast, while 119 variants were defined as PGVs in DDR genes based on the ClinVar and CADD scoring systems, the definition of pathogenic variants is known to be affected by differences in sequencing technology and analysis pipelines.4 Integrated analysis of DNA and mRNA sequences may further improve the interpretation of these germline variants. Although POLQ was identified as the most frequently mutated gene among PGVs in their cohort, it was not externally validated in the ICGC cohort. This could be due to the minor frequency of each PGV, and thus, a larger cohort may be required for the accurate estimation of its occurrence. However, the high frequency of PGVs in the DDR pathway in HCC was validated in 2 independent cohorts. Moreover, pan-cancer genome analysis of 10,389 adult cancers showed that PGVs in the HR and nucleotide excision repair pathways appeared to occur at a high frequency in HCC among 33 different cancer types.4 These findings support the importance of profiling PGVs in HCC patients. While HCCs with PGVs in DDR genes were associated with poor DFS, overall survival was not different between HCC patients with or without these variants. These data suggest that PGVs in DDR genes may promote de novo multicentric hepatocarcinogenesis rather than increase malignant tumor potential. Since most of the HCCs in the current study were resectable-stage cancers, further study of advanced-stage HCCs is needed to clarify the role of PGVs in the DDR pathway in HCC progression. In summary, this large-scale in-depth analysis of PGVs in DDR genes using multiethnic cohorts revealed their clinical significance in HCC and revealed a potential novel targeted therapy for HCC patients with PGVs in the HR pathway. This study by An and colleagues may also highlight the importance and potential usefulness of cancer genome profiling in HCC patients for the guidance of personalized therapy.